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May 9, 2018

The “X” in the sex chromosome

Filed under: Genetics,Genomics,mothers-day,science — Razib Khan @ 3:48 pm

There are ~3 billion base pairs in the human genome. Of that ~5% are in the X chromosome. The X is fully functional, unlike the famously hamstrung Y. It harbors one of the longest genes in the human genome, DMD, at 2,300,000 base pairs. In contrast, the human Y chromosome only has 72 protein coding genes! (it’s perhaps no surprise that, aside from sex determination, many of these genes are involved in things such as spermatogenesis)

And yet it is the Y chromosome which gets full treatment in popular science books. Like the C student who receives praise for a B-, the Y chromosome is given high marks simply for doing a few things here and there, most especially its role in driving the emergence of biological males. But the reality is that males would not be viable if it wasn’t for the X.

Can you see that it says 74?

Because the Y chromosome is so handicapped, filled with repetitive “junk DNA,” the heavy-lifting is shifted onto the single X that males carry. Though the Y is what makes males male, the X is what keeps males alive.

Anyone familiar with sex-linked characteristics knows this. Red-green color blindness is found 8 percent of human males and 0.6 percent of human females. Many more women are carriers of color blindness than who are color blind themselves.

The genes responsible for detection of some colors are found on the X chromosome, and are subject to high mutation rates. If a female has a broken copy she usually has a fallback in a functional second copy. She’s a carrier. In contrast, because males have only one X chromosome (inherited from their mother), they don’t have a backup. If a color-vision gene on the X chromosome is broken, then they’re out of luck when it comes to perceiving the full vibrancy of the world.

In other words, the male X chromosome does not possess recessive traits. All traits express due to the state of the single copy of the gene determining the trait. Every mutation on the X chromosome can potentially produce a mutant that will be exposed to natural selection.

Neanderthal-modern human hybrid

This results in some interesting evolutionary quirks when it comes to how natural selection shapes the genome and drives adaptation within populations and speciation between them. Crosses between different species can leave hybrids infertile. In mammals this often happens in males because mutations on the X chromosome can interfere with proper reproductive development. Selection against the genes of other species then happens because males can’t produce offspring.

Studies of Neanderthal admixture confirm this — there is far less Neanderthal ancestry on the X chromosome than across the rest of the genome. There is strong selection against Neanderthal variants in males, because these genes work less well with the rest of the modern human genome.

A wife of Genghis Khan

But the X chromosome is not distinctive just in terms of just natural selection. As two out of three X chromosomes in any population are found in females, its genetic history will be biased toward that sex. Differences between the X chromosome and the non-sex genome can tell us differences in the histories of men and women.

For example historically many more of the female ancestors of admixed people of the New World tended to be non-European, whether it was indigenous or African. As such, the genetic profile of the X chromosome in terms of similarity to worldwide variation would be different from the non-sex chromosomes, because those come equally from the father and mother. This is exactly what we see. There is less European ancestry on the X chromosome.

More generally mating systems such as polygyny — men having multiple female partners — result in far fewer males than females who contribute to future generations. Among Mongols during the era of Genghis Khan, a small number of males descended from Genghis and his Mongol horde had children with numerous women. Because X chromosomes tend to found in women, more of whom are reproducing, they will more diverse than non-sex chromosomes (where a few men contribute half the genes), while the Y chromosome will be the least diverse of all (where only a few men contribute genetic variation).

Men have only one X chromosome, but the one they have is genetically essential to them. X chromosomes are not exclusive to women, but for all males they are the singular legacy of their mothers. Because of this bias the X can shed light on the history of the women of our species, while the uniqueness of inheritance the X chromosome may even extend to driving the emergence of our species.

Explore your Neanderthal story today.


The “X” in the sex chromosome was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

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